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- PDB-6qrh: High pressure structure of bovine insulin (100 MPa) -

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Basic information

Entry
Database: PDB / ID: 6qrh
TitleHigh pressure structure of bovine insulin (100 MPa)
Components(Insulin) x 2
KeywordsHORMONE / glucose metabolism
Function / homology
Function and homology information


estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate ...estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / positive regulation of protein secretion / insulin receptor binding / response to nutrient levels / hormone activity / positive regulation of insulin secretion / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.152 Å
AuthorsKurpiewska, K. / Milaczewska, A. / Lewinski, K.
CitationJournal: J.Mol.Struct. / Year: 2020
Title: Insulin conformational changes under high pressure in structural studies and molecular dynamics simulations
Authors: Kurpiewska, K. / Milaczewska, A. / Lewinski, K.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7442
Polymers5,7442
Non-polymers00
Water37821
1
A: Insulin
B: Insulin

A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)11,4874
Polymers11,4874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_545-x,-y-1/2,z1
Buried area4330 Å2
ΔGint-37 kcal/mol
Surface area5350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.380, 78.380, 78.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide Insulin


Mass: 2339.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01317
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.01 M Na3 EDTA, 0.1 M Na2HEDTA

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 0.7107 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 15, 2011
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 2.15→16 Å / Num. all: 7347 / Num. obs: 4461 / % possible obs: 99.3 % / Redundancy: 1.6 % / CC1/2: 0.973 / Rmerge(I) obs: 0.131 / Net I/σ(I): 4.7
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 402 / CC1/2: 0.656 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
CrysalisProdata collection
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BN3

2bn3


Resolution: 2.152→15.999 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 454 10.2 %RANDOM
Rwork0.1926 ---
obs0.197 4452 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.152→15.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 0 21 421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008433
X-RAY DIFFRACTIONf_angle_d0.859591
X-RAY DIFFRACTIONf_dihedral_angle_d2.925294
X-RAY DIFFRACTIONf_chiral_restr0.0562
X-RAY DIFFRACTIONf_plane_restr0.00778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1525-2.46290.30161380.27171330X-RAY DIFFRACTION99
2.4629-3.09930.28521490.22641320X-RAY DIFFRACTION99
3.0993-15.99970.18471670.14441348X-RAY DIFFRACTION99

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